UGENE Forum - De-novo assembly of Sanger data, creating consensus with quality values using CAP3

Apr 20^th, 2024 at 2:15pm

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De-novo assembly of Sanger data, creating consensus with quality values using CAP3 (Read 782 times)

Apr 18^th, 2023 at 9:14am

genomesss Offline
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Posts: 1

Hi all,

I have Sanger sequencing data (ab1 files) which I would like to de-novo assemble into a consensus sequence. However, I would also like to obtain the quality values for the consensus as it is possible with the stand-alone program CAP3, however, when I use it within UGENE I cannot figure out how to obtain those quality values.

Any help would be appreciated!
Thanks!

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Reply #1 - Apr 18^th, 2023 at 12:06pm

Dmitrii Sukhomlinov Offline
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Russia

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Posts: 76

Hello,

Unfortunately, for now, UGENE do not support quality values, but we know about it and will try to add this feature in the future. CAP3 exists in UGENE (Tools -> Sanger data analysis -> Reads de novo assembly (with CAP3)) and uses quality values, but UGENE just do not show them.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.

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